Re: [AMBER] nmode: dihedral angle error

From: case <>
Date: Fri, 26 Nov 2010 09:46:12 -0500

On Mon, Nov 22, 2010, Michael Petersen wrote:
> After the sander minimization I have attempted Newton-Raphson
> minimization with nmode.

> DIHEDRAL ANGLE ERROR: 1 90 93 102 105

This is a misleading message, since it is not really an error.

However, I'd recommend using the xmin minimizer (should eliminate the need to
do Newton-Raphson at all), and using the nmode() facility in NAB: the latter
allows you to use the GB solvent model (rather than epsilon=4r), and has
better performance and memory utilization. We don't really support the
original nmode code any more.

...good luck....dac

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Received on Fri Nov 26 2010 - 07:00:06 PST
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